1-171090009-C-G

Variant names:

• chr1-171090009-C-G
• rs1736560
• ENST00000896149.1:c.-6-2644C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000896149.1(FMO3):​c.-6-2644C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 151,684 control chromosomes in the GnomAD database, including 6,963 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.29 (6963 hom., cov: 31)
• Consequence: FMO3 ENST00000896149.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650
• Publications: 7 publications found

Genes affected

FMO3 (HGNC:3771): (flavin containing dimethylaniline monoxygenase 3) Flavin-containing monooxygenases (FMO) are an important class of drug-metabolizing enzymes that catalyze the NADPH-dependent oxygenation of various nitrogen-,sulfur-, and phosphorous-containing xenobiotics such as therapeutic drugs, dietary compounds, pesticides, and other foreign compounds. The human FMO gene family is composed of 5 genes and multiple pseudogenes. FMO members have distinct developmental- and tissue-specific expression patterns. The expression of this FMO3 gene, the major FMO expressed in adult liver, can vary up to 20-fold between individuals. This inter-individual variation in FMO3 expression levels is likely to have significant effects on the rate at which xenobiotics are metabolised and, therefore, is of considerable interest to the pharmaceutical industry. This transmembrane protein localizes to the endoplasmic reticulum of many tissues. Alternative splicing of this gene results in multiple transcript variants encoding different isoforms. Mutations in this gene cause the disorder trimethylaminuria (TMAu) which is characterized by the accumulation and excretion of unmetabolized trimethylamine and a distinctive body odor. In healthy individuals, trimethylamine is primarily converted to the non odorous trimethylamine N-oxide.[provided by RefSeq, Jan 2016]

FMO3 Gene-Disease associations (from GenCC):

• trimethylaminuria

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• severe primary trimethylaminuria

  Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)

FMO1-AS1 (HGNC:40240):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000896149.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FMO3	ENST00000896149.1		c.-6-2644C>G		intron	N/A	ENSP00000566208.1
	FMO1-AS1	ENST00000653116.1		n.542+78095G>C		intron	N/A
	FMO1-AS1	ENST00000664920.1		n.681+31741G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44518 AN: 151570 Hom.: 6943 Cov.: 31

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.274

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.294 AC: 44564 AN: 151684 Hom.: 6963 Cov.: 31 AF XY: 0.299 AC XY: 22139 AN XY: 74114

African (AFR) AF: 0.215 AC: 8909 AN: 41344

American (AMR) AF: 0.372 AC: 5677 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1002 AN: 3466

East Asian (EAS) AF: 0.576 AC: 2973 AN: 5158

South Asian (SAS) AF: 0.309 AC: 1487 AN: 4806

European-Finnish (FIN) AF: 0.305 AC: 3190 AN: 10444

Middle Eastern (MID) AF: 0.257 AC: 74 AN: 288

European-Non Finnish (NFE) AF: 0.300 AC: 20404 AN: 67920

Other (OTH) AF: 0.276 AC: 582 AN: 2108

Alfa AF: 0.170 Hom.: 359

Bravo AF: 0.293

Asia WGS AF: 0.438 AC: 1517 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.89
DANN	Benign	0.50
PhyloP100		-0.065

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1736560; hg19: chr1-171059150;